Bio::DB::GFF::Adaptor::biofetch -- Cache BioFetch objects in a Bio::DB::GFF database
Proof of principle. Not for production use.
This adaptor is a proof-of-principle. It is used to fetch BioFetch sequences into a Bio::DB::GFF database (currently uses a hard-coded EMBL database) as needed. This allows the Generic Genome Browser to be used as a Genbank/EMBL browser.
Lincoln Stein <lstein@cshl.org>.
Copyright 2002 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
Title : new Usage : $db = Bio::DB::GFF->new(-adaptor=>'biofetch',@args) Function: create a new adaptor Returns : a Bio::DB::GFF object Args : see below Status : Public
This is the constructor for the adaptor. It is called automatically by Bio::DB::GFF->new. In addition to arguments that are common among all adaptors, the following class-specific arguments are recgonized:
Argument Description -------- ----------- -dsn the DBI data source, e.g. 'dbi:mysql:ens0040' -user username for authentication -pass the password for authentication -proxy [['http','ftp'],'http://proxy:8080']
-dsn,-user and -pass indicate the local database to cache results in, and as are per Bio::DB::GFF::Adaptor::dbi. The -proxy argument allows you to set the biofetch web proxy, and uses the same syntax described for the proxy() method of Bio::DB::WebDBSeqI, except that the argument must be passed as an array reference.
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.